private static string GetDisplayText(ProteinDisplayMode arg, ProteinMetadata proteinMetadata)
{
string val;
switch (arg)
{
case ProteinDisplayMode.ByAccession:
val = proteinMetadata.Accession;
break;
case ProteinDisplayMode.ByGene:
val = proteinMetadata.Gene;
break;
case ProteinDisplayMode.ByPreferredName:
val = proteinMetadata.PreferredName;
break;
default:
val = proteinMetadata.Name;
break;
}
Assert.IsFalse(String.IsNullOrEmpty(val));
if (arg != ProteinDisplayMode.ByName)
{
Assert.AreNotEqual(val, proteinMetadata.Name);
}
return(val);
}
public static string ProteinModalDisplayText(ProteinMetadata metadata, ProteinDisplayMode displayProteinsMode)
{
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
case ProteinDisplayMode.ByPreferredName:
case ProteinDisplayMode.ByGene:
break;
default:
return(metadata.Name);
}
// If the desired field is not populated because it's not yet searched, say so
if (metadata.NeedsSearch())
{
return(Resources.ProteinMetadataManager_LookupProteinMetadata_resolving_protein_details);
}
// If the desired field is not populated, return something like "<name: YAL01234>"
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, metadata.Name);
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
return(metadata.Accession ?? failsafe);
case ProteinDisplayMode.ByPreferredName:
return(metadata.PreferredName ?? failsafe);
case ProteinDisplayMode.ByGene:
return(metadata.Gene ?? failsafe);
}
return(failsafe);
}
public DbProteinName(DbProtein protein, ProteinMetadata proteinMetadata)
{
// ReSharper disable DoNotCallOverridableMethodsInConstructor
IsPrimary = (protein == null);
Protein = protein;
// ReSharper restore DoNotCallOverridableMethodsInConstructor
_proteinMetadata = proteinMetadata ?? ProteinMetadata.EMPTY;
}
public FastaSequence AddAlternative(ProteinMetadata proteinMetadata)
{
var alternativesNew = new List <ProteinMetadata>(Alternatives)
{
proteinMetadata
};
return(new FastaSequence(_name, _description, alternativesNew, _sequence, _isDecoy));
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
if (Equals(id.Name, proteinMetadata.Name))
proteinMetadata = proteinMetadata.ChangeName(null); // Make it clear that the name hasn't been altered
if (Equals(id.Description, proteinMetadata.Description))
proteinMetadata = proteinMetadata.ChangeDescription(null); // Make it clear that the description hasn't been altered
_proteinMetadata = proteinMetadata;
}
private void WriteProteinMetadataXML(XmlWriter writer, ProteinMetadata proteinMetadata, bool skipNameAndDescription)
{
if (!skipNameAndDescription)
{
writer.WriteAttributeIfString(ATTR.name, proteinMetadata.Name);
writer.WriteAttributeIfString(ATTR.description, proteinMetadata.Description);
}
writer.WriteAttributeIfString(ATTR.accession, proteinMetadata.Accession);
writer.WriteAttributeIfString(ATTR.gene, proteinMetadata.Gene);
writer.WriteAttributeIfString(ATTR.species, proteinMetadata.Species);
writer.WriteAttributeIfString(ATTR.preferred_name, proteinMetadata.PreferredName);
writer.WriteAttributeIfString(ATTR.websearch_status, proteinMetadata.WebSearchInfo.ToString());
}
public PeptideGroupDocNode ChangeProteinMetadata(ProteinMetadata proteinMetadata)
{
var newMetadata = proteinMetadata;
if (Equals(PeptideGroup.Name, newMetadata.Name))
{
newMetadata = newMetadata.ChangeName(null); // no actual override
}
if (Equals(PeptideGroup.Description, newMetadata.Description))
{
newMetadata = newMetadata.ChangeDescription(null); // no actual override
}
return(ChangeProp(ImClone(this), im => im._proteinMetadata = newMetadata));
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: base(id, annotations, children, autoManageChildren)
{
if (Equals(id.Name, proteinMetadata.Name))
{
proteinMetadata = proteinMetadata.ChangeName(null); // Make it clear that the name hasn't been altered
}
if (Equals(id.Description, proteinMetadata.Description))
{
proteinMetadata = proteinMetadata.ChangeDescription(null); // Make it clear that the description hasn't been altered
}
_proteinMetadata = proteinMetadata;
}
public FastaSequence GetFastaSequence(String proteinName, out ProteinMetadata foundMetadata)
{
foundMetadata = null;
if (IsNone)
{
return(null);
}
using (var proteomeDb = OpenProteomeDb())
{
Protein protein = proteomeDb.GetProteinByName(proteinName);
if (protein == null)
{
return(null);
}
foundMetadata = protein.ProteinMetadata;
return(MakeFastaSequence(protein));
}
}
public FastaSequence GetFastaSequence(String proteinName, out ProteinMetadata foundMetadata)
{
foundMetadata = null;
if (IsNone)
{
return(null);
}
using (var proteomeDb = OpenProteomeDb())
{
Protein protein = proteomeDb.GetProteinByName(proteinName);
if (protein == null)
{
return(null);
}
List <ProteinMetadata> alternativeProteins = new List <ProteinMetadata>();
foreach (var alternativeName in protein.AlternativeNames)
{
alternativeProteins.Add(alternativeName);
}
foundMetadata = protein.ProteinMetadata;
return(new FastaSequence(protein.ProteinMetadata.Name, protein.ProteinMetadata.Description, alternativeProteins, protein.Sequence));
}
}
public PeptideGroupDocNode(PeptideGroup id, Annotations annotations, ProteinMetadata proteinMetadata,
PeptideDocNode[] children, bool autoManageChildren)
: this(id, annotations, proteinMetadata, children, autoManageChildren, null)
{
}
public static string ProteinModalDisplayText(ProteinMetadata metadata, string displayProteinsMode)
{
return(ProteinModalDisplayText(metadata, ProteinsDisplayMode(displayProteinsMode)));
}
private static string GetDisplayText(ProteinDisplayMode arg, ProteinMetadata proteinMetadata)
{
string val;
switch (arg)
{
case ProteinDisplayMode.ByAccession:
val = proteinMetadata.Accession;
break;
case ProteinDisplayMode.ByGene:
val = proteinMetadata.Gene;
break;
case ProteinDisplayMode.ByPreferredName:
val = proteinMetadata.PreferredName;
break;
default:
val = proteinMetadata.Name;
break;
}
Assert.IsFalse(String.IsNullOrEmpty(val));
if (arg != ProteinDisplayMode.ByName)
Assert.AreNotEqual(val, proteinMetadata.Name);
return val;
}
[MethodImpl(MethodImplOptions.NoOptimization)] // TODO(nicksh): reenable optimizations after we track down a NullReferenceException
public static IList <ListViewItem> CreateListViewItems(IList <ProteinMatch> matches, String searchText, ProteinMatchTypes matchTypes, PeptideSettings peptideSettings, int maxCount)
{
var listItems = new SortedList <string, ListViewItem>();
var setUsedMatches = new HashSet <string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (matchTypes.Contains(ProteinMatchType.sequence))
{
HashSet <String> addedPeptideSequences = new HashSet <string>();
FastaSequence fastaSequence;
try
{
fastaSequence = new FastaSequence("name", "description", new ProteinMetadata[0], match.Protein.Sequence); // Not L10N
}
catch (InvalidDataException)
{
// It's possible that the peptide sequence in the fasta file was bogus, in which case we just don't digest it.
continue;
}
foreach (Peptide peptide in peptideSettings.Enzyme.Digest(fastaSequence, peptideSettings.DigestSettings))
{
if (!peptide.Sequence.StartsWith(searchText))
{
continue;
}
if (!addedPeptideSequences.Add(peptide.Sequence))
{
continue;
}
var listItem = new ListViewItem
{
Text = peptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = peptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
setUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.peptide;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes));
foreach (var name in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(name.TextForMatchTypes(matchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// Note the leading space in this sort key - we'd like to list sequence matches first
var key = TextUtil.SpaceSeparate(" ", listItem.Text, listItem.ToolTipText); // Not L10N
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Decide which field not to display on righthand side, based on what's already showing on the left due to View|Targets|By* menu
ProteinMatchTypes displayMatchTypes = ProteinMatchTypes.ALL;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinMetadataManager.ProteinDisplayMode.ByName:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.name);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByAccession:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.accession);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByGene:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.gene);
break;
case ProteinMetadataManager.ProteinDisplayMode.ByPreferredName:
displayMatchTypes = displayMatchTypes.Except(ProteinMatchType.preferredName);
break;
}
ProteinMatchTypes secondPassMatchTypes = matchTypes.Except(
ProteinMatchType.sequence, // We already did sequence
ProteinMatchType.description); // And aren't ready for description
foreach (var match in matches)
{
if (setUsedMatches.Contains(match.Protein.Name))
{
continue;
}
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
foreach (ProteinMatchType tryType in secondPassMatchTypes)
{
if (match.MatchTypes.Contains(tryType))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = ProteinMetadataManager.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.AlternativeName, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchTypes.Except(ProteinMatchType.name)), searchText);
}
else
{
listItem.Text = ProteinMetadataManager.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchTypes), searchText);
}
setUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchTypes));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// We want the sort to be on the particular bit of metadata that we matched
var key = TextUtil.SpaceSeparate(match.Protein.ProteinMetadata.TextForMatchTypes(ProteinMatchTypes.Singleton(tryType)),
listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
break;
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Any matches by description?
foreach (var match in matches)
{
if (setUsedMatches.Contains(match.Protein.Name))
{
continue;
}
if (match.MatchTypes.Contains(ProteinMatchType.description))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (matchName != null && matchName.Length > MAX_NAME_LENGTH)
{
proteinInfo = proteinInfo.ChangeName(matchName.Substring(0, MAX_NAME_LENGTH) + "..."); // Not L10N
}
var alternativeNames = new List <ProteinMetadata>();
if (mainName == null)
{
mainName = proteinInfo;
}
else
{
alternativeNames.Add(proteinInfo);
}
var listItem = new ListViewItem
{
Text = ProteinMetadataManager.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int)ImageId.protein,
Tag = new StatementCompletionItem {
ProteinInfo = proteinInfo, SearchText = searchText
}
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchTypes), searchText);
if (match.Protein.AlternativeNames.Count > 0)
{
alternativeNames.AddRange(match.Protein.AlternativeNames);
StringBuilder tooltip = new StringBuilder(Resources.StatementCompletionTextBox_CreateListViewItems_Alternative_Names);
foreach (var altName in alternativeNames)
{
if (altName.Name == mainName.Name)
{
continue;
}
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchTypes.Union(ProteinMatchType.name)));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
}
// We want the sort to be on what we matched in the description, and what follows.
var remains = match.Protein.ProteinMetadata.Description ?? string.Empty;
int pos = remains.ToLower().IndexOf(searchText.ToLower(), StringComparison.Ordinal);
if (pos > 0)
{
remains = remains.Substring(pos);
}
var key = TextUtil.SpaceSeparate(remains, listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
return(new List <ListViewItem>(listItems.Values));
}
public FastaSequence GetFastaSequence(String proteinName, out ProteinMetadata foundMetadata)
{
foundMetadata = null;
if (IsNone)
return null;
using (var proteomeDb = OpenProteomeDb())
{
Protein protein = proteomeDb.GetProteinByName(proteinName);
if (protein == null)
{
return null;
}
List<ProteinMetadata> alternativeProteins = new List<ProteinMetadata>();
foreach (var alternativeName in protein.AlternativeNames)
{
alternativeProteins.Add(alternativeName);
}
foundMetadata = protein.ProteinMetadata;
return new FastaSequence(protein.ProteinMetadata.Name, protein.ProteinMetadata.Description, alternativeProteins, protein.Sequence);
}
}
public DbProtein(ProteinMetadata other)
{
_proteinMetadata = other;
}
public virtual void SetWebSearchCompleted()
{
// Prepend the "done" tag to the searchterm/history.
_proteinMetadata = _proteinMetadata.SetWebSearchCompleted();
}
public void ChangeProteinMetadata(ProteinMetadata other)
{
ProteinDbInfo.ChangeProteinMetadata(other);
}
public virtual void SetWebSearchTerm(WebSearchTerm search)
{
_proteinMetadata = _proteinMetadata.SetWebSearchTerm(search);
}
private FastaSequence GetFastaSequence(DataGridViewRow row, string proteinName, out ProteinMetadata metadata)
{
metadata = null;
var backgroundProteome = GetBackgroundProteome(DocumentUiContainer.DocumentUI);
if (backgroundProteome.IsNone)
return null;
var fastaSequence = backgroundProteome.GetFastaSequence(proteinName, out metadata);
if (fastaSequence == null)
{
// Sometimes the protein name in the background proteome will have an extra "|" on the end.
// In that case, update the name of the protein to match the one in the database.
fastaSequence = backgroundProteome.GetFastaSequence(proteinName + "|"); // Not L10N
if (fastaSequence != null)
{
row.Cells[colPeptideProtein.Index].Value = fastaSequence.Name;
}
}
return fastaSequence;
}
public virtual ProteinMetadata ClearWebSearchInfo()
{
// Sometimes you really just want to initialize, not have a search history.
_proteinMetadata = _proteinMetadata.ClearWebSearchInfo();
return(_proteinMetadata);
}
public virtual ProteinMetadata MergeProteinMetadata(DbProteinName other)
{
_proteinMetadata = _proteinMetadata.Merge(other.GetProteinMetadata());
return(_proteinMetadata);
}
public virtual ProteinMetadata ChangeProteinMetadata(ProteinMetadata other)
{
_proteinMetadata = other;
return(_proteinMetadata);
}
public PeptideGroupDocNode(PeptideGroup id, ProteinMetadata proteinMetadata, PeptideDocNode[] children)
: this(id, Annotations.EMPTY, proteinMetadata, children, true)
{
}
public PeptideGroupDocNode ChangeProteinMetadata(ProteinMetadata proteinMetadata)
{
var newMetadata = proteinMetadata;
if (Equals(PeptideGroup.Name, newMetadata.Name))
newMetadata = newMetadata.ChangeName(null); // no actual override
if (Equals(PeptideGroup.Description, newMetadata.Description))
newMetadata = newMetadata.ChangeDescription(null); // no actual override
return ChangeProp(ImClone(this), im => im._proteinMetadata = newMetadata);
}
public PeptideGroupDocNode(PeptideGroup id, ProteinMetadata proteinMetadata, PeptideDocNode[] children)
: this(id, Annotations.EMPTY, proteinMetadata, children, true)
{
}
public DbProtein()
{
_proteinMetadata = ProteinMetadata.EMPTY;
}
public DbProtein(ProteinMetadata other)
{
_proteinMetadata = other;
}
private static bool Matches(ProteinMetadata proteinMetadata, ProteinMatchType matchType, string ltext)
{
return ContainsLowerCase(proteinMetadata.TextForMatchTypes(matchType), ltext);
}
private SrmDocument AddProteins(SrmDocument document, ref IdentityPath selectedPath)
{
if (tabControl1.SelectedTab != tabPageProteinList)
return document;
var backgroundProteome = GetBackgroundProteome(document);
for (int i = gridViewProteins.Rows.Count - 1; i >= 0; i--)
{
var row = gridViewProteins.Rows[i];
var proteinName = Convert.ToString(row.Cells[colProteinName.Index].Value);
if (String.IsNullOrEmpty(proteinName))
{
continue;
}
var pastedMetadata = new ProteinMetadata(proteinName,
Convert.ToString(row.Cells[colProteinDescription.Index].Value),
NullForEmpty(Convert.ToString(row.Cells[colProteinPreferredName.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinAccession.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinGene.Index].Value)),
NullForEmpty(Convert.ToString(row.Cells[colProteinSpecies.Index].Value)));
FastaSequence fastaSequence = null;
if (!backgroundProteome.IsNone)
{
ProteinMetadata protdbMetadata;
fastaSequence = backgroundProteome.GetFastaSequence(proteinName, out protdbMetadata);
// Fill in any gaps in pasted metadata with that in protdb
pastedMetadata = pastedMetadata.Merge(protdbMetadata);
}
// Strip any whitespace (tab, newline etc) In case it was copied out of a FASTA file
var fastaSequenceString = new string(Convert.ToString(row.Cells[colProteinSequence.Index].Value).Where(c => !Char.IsWhiteSpace(c)).ToArray());
if (!string.IsNullOrEmpty(fastaSequenceString))
{
try
{
if (fastaSequence == null) // Didn't match anything in protdb
{
fastaSequence = new FastaSequence(pastedMetadata.Name, pastedMetadata.Description,
new ProteinMetadata[0], fastaSequenceString);
}
else
{
if (fastaSequence.Sequence != fastaSequenceString)
{
fastaSequence = new FastaSequence(pastedMetadata.Name, pastedMetadata.Description,
fastaSequence.Alternatives, fastaSequenceString);
}
}
}
catch (Exception exception)
{
ShowProteinError(new PasteError
{
Line = i,
Column = colProteinDescription.Index,
Message = string.Format(Resources.PasteDlg_AddProteins_Invalid_protein_sequence__0__, exception.Message)
});
return null;
}
}
if (fastaSequence == null)
{
ShowProteinError(
new PasteError
{
Line = i,
Message = backgroundProteome.IsNone
? Resources.PasteDlg_AddProteins_Missing_protein_sequence
: Resources.PasteDlg_AddProteins_This_protein_was_not_found_in_the_background_proteome_database
});
return null;
}
var description = pastedMetadata.Description;
if (!string.IsNullOrEmpty(description) && description != fastaSequence.Description)
{
fastaSequence = new FastaSequence(fastaSequence.Name, description, fastaSequence.Alternatives, fastaSequence.Sequence);
}
pastedMetadata = pastedMetadata.ChangeName(fastaSequence.Name).ChangeDescription(fastaSequence.Description); // Make sure these agree
var nodeGroupPep = new PeptideGroupDocNode(fastaSequence, pastedMetadata, new PeptideDocNode[0]);
nodeGroupPep = nodeGroupPep.ChangeSettings(document.Settings, SrmSettingsDiff.ALL);
var to = selectedPath;
if (to == null || to.Depth < (int)SrmDocument.Level.MoleculeGroups)
document = (SrmDocument)document.Add(nodeGroupPep);
else
{
Identity toId = selectedPath.GetIdentity((int)SrmDocument.Level.MoleculeGroups);
document = (SrmDocument)document.Insert(toId, nodeGroupPep);
}
selectedPath = new IdentityPath(nodeGroupPep.Id);
}
return document;
}
public static string ProteinModalDisplayText(ProteinMetadata metadata, string displayProteinsMode)
{
return ProteinModalDisplayText(metadata, ProteinsDisplayMode(displayProteinsMode));
}
private PeptideGroupDocNode GetMoleculePeptideGroup(SrmDocument document, DataGridViewRow row, bool requireProductInfo)
{
var pepGroup = new PeptideGroup();
var pep = GetMoleculePeptide(document, row, pepGroup, requireProductInfo);
if (pep == null)
return null;
var name = Convert.ToString(row.Cells[INDEX_MOLECULE_GROUP].Value);
if (string.IsNullOrEmpty(name))
name = document.GetPeptideGroupId(true);
var metadata = new ProteinMetadata(name, string.Empty).SetWebSearchCompleted(); // FUTURE: some kind of lookup for small molecules
return new PeptideGroupDocNode(pepGroup, metadata, new[] {pep});
}
public static string ProteinModalDisplayText(ProteinMetadata metadata, ProteinDisplayMode displayProteinsMode)
{
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
case ProteinDisplayMode.ByPreferredName:
case ProteinDisplayMode.ByGene:
break;
default:
return metadata.Name;
}
// If the desired field is not populated because it's not yet searched, say so
if (metadata.NeedsSearch())
return Resources.ProteinMetadataManager_LookupProteinMetadata_resolving_protein_details;
// If the desired field is not populated, return something like "<name: YAL01234>"
var failsafe = String.Format(Resources.PeptideGroupTreeNode_ProteinModalDisplayText__name___0__, metadata.Name);
switch (displayProteinsMode)
{
case ProteinDisplayMode.ByAccession:
return metadata.Accession ?? failsafe;
case ProteinDisplayMode.ByPreferredName:
return metadata.PreferredName ?? failsafe;
case ProteinDisplayMode.ByGene:
return metadata.Gene ?? failsafe;
}
return failsafe;
}
public ProteinMetadata ParseProteinMetaData(ProteinMetadata proteinMetadata)
{
if (proteinMetadata.Name == null)
return null;
// watch for inputs like name="Library Peptides" which clearly isn't an actual protein name
if (proteinMetadata.Name.Contains(" ")) // Not L10N
return null;
return ParseProteinMetaData(proteinMetadata.Name + " " + proteinMetadata.Description); // Not L10N
}
public DbProtein()
{
_proteinMetadata = ProteinMetadata.EMPTY;
}
private ProteinMetadata MergeSearchResult(ProteinMetadata searchResult, ProteinMetadata original)
{
// like a normal merge, use update to fill gaps in current, but
// then prefer the update name and description
// we do this to make it easier for user to relate back to the original
// fasta header line while still allowing for cases where there may not
// possibly have been a proper original source for descrption or even name
ProteinMetadata result = searchResult.Merge(original);
if (!String.IsNullOrEmpty(original.Name))
result = result.ChangeName(original.Name);
if (!String.IsNullOrEmpty(original.Description))
result = result.ChangeDescription(original.Description);
return result;
}
/// <summary>
/// Create the ordered list of dropdown items, with a rational sort order:
/// First present any sequence matches, sorted by sequence
/// Then present any name, accession, gene, preferredname, or species metadata matches, sorted by the matched metadata field
/// Then present any matches against the description field, sorted by the description text starting at the match location
/// </summary>
public static IList <ListViewItem> CreateListViewItems(IList <ProteinMatch> matches, String searchText, ProteinMatchType matchTypes, int maxCount)
{
var listItems = new SortedList <string, ListViewItem>();
var listUsedMatches = new List <string>();
// First check for matching by sequence
foreach (var match in matches)
{
if (0 != (matchTypes & match.MatchType & ProteinMatchType.sequence))
{
foreach (DigestedPeptide digestedPeptide in match.DigestedPeptides)
{
var listItem = new ListViewItem
{
Text = digestedPeptide.Sequence,
Tag = new StatementCompletionItem
{
Peptide = digestedPeptide.Sequence,
ProteinInfo = match.Protein.ProteinMetadata,
SearchText = searchText
},
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes),
null);
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.peptide;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(matchTypes));
foreach (var name in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(name.TextForMatchTypes(matchTypes));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// Note the leading space in this sort key - we'd like to list sequence matches first
var key = TextUtil.SpaceSeparate(" ", listItem.Text, listItem.ToolTipText); // Not L10N
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Decide which field not to display on righthand side, based on what's already showing on the left due to View|Targets|By* menu
ProteinMatchType displayMatchType = ProteinMatchType.all;
switch (SequenceTree.ProteinsDisplayMode)
{
case ProteinDisplayMode.ByName:
displayMatchType &= ~ProteinMatchType.name;
break;
case ProteinDisplayMode.ByAccession:
displayMatchType &= ~ProteinMatchType.accession;
break;
case ProteinDisplayMode.ByGene:
displayMatchType &= ~ProteinMatchType.gene;
break;
case ProteinDisplayMode.ByPreferredName:
displayMatchType &= ~ProteinMatchType.preferredName;
break;
}
foreach (var match in matches)
{
// Try matching on name, accession etc - cycle through name, accession, preferredName, gene
for (int bit = 1; bit < (int)ProteinMatchType.all; bit = bit << 1)
{
ProteinMatchType tryType = (ProteinMatchType)bit;
if ((tryType != ProteinMatchType.sequence) && // We already did sequence
(tryType != ProteinMatchType.description) && // And aren't ready for description
(0 != (matchTypes & match.MatchType & tryType) &&
!listUsedMatches.Contains(match.Protein.Name)))
{
var listItem = new ListViewItem();
// Show description, and any other fields we were searching on
if (match.AlternativeName != null)
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.AlternativeName, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.AlternativeName, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.AlternativeName.TextForMatchTypes(displayMatchType & ~ProteinMatchType.name), searchText);
}
else
{
listItem.Text = PeptideGroupTreeNode.ProteinModalDisplayText(match.Protein.ProteinMetadata, Settings.Default.ShowPeptidesDisplayMode);
listItem.Tag = new StatementCompletionItem {
ProteinInfo = match.Protein.ProteinMetadata, SearchText = searchText
};
StatementCompletionForm.AddDescription(listItem,
match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType), searchText);
}
listUsedMatches.Add(match.Protein.Name);
listItem.ImageIndex = (int)ImageId.protein;
var tooltip = new StringBuilder();
tooltip.AppendLine(Resources.StatementCompletionTextBox_CreateListViewItems_Descriptions)
.Append(match.Protein.ProteinMetadata.TextForMatchTypes(displayMatchType));
foreach (var altName in match.Protein.AlternativeNames)
{
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
// We want the sort to be on the particular bit of metadata that we matched
var key = TextUtil.SpaceSeparate(match.Protein.ProteinMetadata.TextForMatchTypes(tryType), listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
break;
}
}
}
if (listItems.Count >= maxCount)
{
return(new List <ListViewItem>(listItems.Values)); // We used to exit here if we had any matches - but that's frustrating when you're not actually trying to match by sequence
}
// Any matches by description?
foreach (var match in matches)
{
if ((0 != (match.MatchType & ProteinMatchType.description)) &&
!listUsedMatches.Contains(match.Protein.Name))
{
ProteinMetadata mainName = match.AlternativeDescription;
string matchName = match.Protein.Name;
var proteinInfo = match.Protein.ProteinMetadata;
if (matchName.Length > MAX_NAME_LENGTH)
{
proteinInfo = proteinInfo.ChangeName(matchName.Substring(0, MAX_NAME_LENGTH) + "..."); // Not L10N
}
var alternativeNames = new List <ProteinMetadata>();
if (mainName == null)
{
mainName = proteinInfo;
}
else
{
alternativeNames.Add(proteinInfo);
}
var listItem = new ListViewItem
{
Text = PeptideGroupTreeNode.ProteinModalDisplayText(mainName, Settings.Default.ShowPeptidesDisplayMode),
ImageIndex = (int)ImageId.protein,
Tag = new StatementCompletionItem {
ProteinInfo = proteinInfo, SearchText = searchText
}
};
StatementCompletionForm.AddDescription(listItem, mainName.TextForMatchTypes(displayMatchType), searchText);
if (match.Protein.AlternativeNames.Count > 0)
{
alternativeNames.AddRange(match.Protein.AlternativeNames);
StringBuilder tooltip = new StringBuilder(Resources.StatementCompletionTextBox_CreateListViewItems_Alternative_Names);
foreach (var altName in alternativeNames)
{
if (altName.Name == mainName.Name)
{
continue;
}
tooltip.AppendLine().Append(altName.TextForMatchTypes(displayMatchType | ProteinMatchType.name));
}
listItem.ToolTipText = StripTabs(tooltip.ToString());
}
// We want the sort to be on what we matched in the description, and what follows.
var remains = match.Protein.ProteinMetadata.Description;
int pos = remains.ToLower().IndexOf(searchText.ToLower(), StringComparison.Ordinal);
if (pos > 0)
{
remains = remains.Substring(pos);
}
var key = TextUtil.SpaceSeparate(remains, listItem.Text, listItem.ToolTipText);
if (!listItems.ContainsKey(key))
{
listItems.Add(key, listItem);
}
}
}
return(new List <ListViewItem>(listItems.Values));
}
